What Does Windown Size Exact Mean When Trimming

Question

[Tonyzeng]

HI I have a question, when I use SLIDINGWINDOW option in trimmomatic, what does exact mean for the windownsize, like SLIDINGWINDOW:4:15, what is 4 mean? I am more familiar with fastx-toolkit, that use percent like 75 mean %75 base must be over the quality like 20. Does this number 4 in slidingwindow has the same function?

Thank you

[Tonyzeng]

suppose my reads have 100bp length, if I want to filter these reads with 80% bases under 20 quality, should I use Slidiningwindow as 80:20, does my understanding right?

Answer 1

[Devon Ryan]

I take it you didn't read the manual. Had you done so, you would have found the following:

Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold. By considering multiple bases, a single poor quality base will not cause the removal of high quality data later in the read.

SLIDINGWINDOW:<windowSize>:<requiredQuality>

[Tonyzeng]

thank you, dpryan79, does my understanding right for the above? 80:20 mean cut off any reads that have 80bases below the 20 quality score?

[Devon Ryan]

Not exactly. It averages the quality scores of the 80 bases. If that average is below 20, then it trims. If you had 79 bases with scores of 19 and 1 base with a score of 110 (not that that would ever occur), then the window wouldn't be trimmed. There's no exact equivalent with slidingwindow in trimmomatic to what you used in fastx-toolkit.